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Outline

Outline. Terminologies Tree reconstruction methods Distance-based (Neighbor-joining) Character-based (Maximum Parsimony, Maximum Likelihood, Bayesian) Hand over to Ben about more serious issues. Phylogeny. why study Phylogeny?. evolution.berkeley.edu. why study Phylogeny?.

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Outline

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  1. Outline • Terminologies • Tree reconstruction methods • Distance-based (Neighbor-joining) • Character-based (Maximum Parsimony, Maximum Likelihood, Bayesian) • Hand over to Ben about more serious issues

  2. Phylogeny

  3. why study Phylogeny? evolution.berkeley.edu

  4. why study Phylogeny? evolution.berkeley.edu

  5. why study Phylogeny?

  6. why study Phylogeny?

  7. why study Phylogeny? HIV trial in Libya

  8. Outgroup Ingroup root node branch clade Time Tree Terminologies Gorillas Chimps Humans Bonobos

  9. Gorillas Chimps Bonobos Humans Bonobos Humans Chimps Rotating the branches by the nodes does not change the hypothesis about the relationship Gorillas Bonobos Gorillas Chimps Humans Time Time Time Most Recent Common Ancestor

  10. Polytomy Unresolved Relationship A B C D Time

  11. How to reconstruct trees... pairwise distance matrix A B C D A B C D C A A+C B D DNA MATRIX A+C C TAXA B A G T TACCTGAC A B C D D B • Distance-based • Neighbor-joining D G AACGGTGAA GT TAGGTGAC A+C B+D CAA TGGACAT A+C B+D C A B D

  12. outgroup A B C D unresolved “polytomy” Parsimony looks for the tree(s) with the minimum number of changes Character-based 0= absent 1= present

  13. outgroup A B C D Parsimony 0= absent 1= present reconstructing tress based on Synapomorphies (Shared Derived Traits) trait 1 evolved here Number of changes = 1 step Trait 1 is a Synapomorphic trait that unites (A, B, C, D)

  14. O A B C D 2 steps required 0= absent 1= present outgroup A C B D trait 2 evolved here trait 2 evolved here Number of changes = 1 step Trait 2 is a Synapomorphic trait that unites (B, D)

  15. Parsimony 0= absent 1= present outgroup C A B D trait 3 evolved here Number of changes = 1 step Trait 3 is a Synapomorphic trait that unites (A, B, D)

  16. Parsimony 0= absent 1= present outgroup C A B D trait 4 evolved here Number of changes = 1 step Trait 4 is an Apomorphic (dervied trait) that is unique to B NOT INFORMATIVE

  17. Parsimony 0= absent 1= present outgroup C A B D trait 5 lost here Number of changes = 1 step Trait 5 is a Plesiomorphic(ancestral trait) to this group NOT INFORMATIVE

  18. Parsimony 0= absent 1= present outgroup C A B D trait 5 lost trait 4 trait 2 trait 3 trait 1 Number of changes = 5 steps Tree Length = 5 This is the Most Parsimonious tree that requires the least number of character evolution (5 steps).

  19. Maximum Likelihood - looks for the tree that maximizes the probability of observing the data given that tree and the model of evolution. You usually get a single tree. Bayesian Analysis - looks for the tree that maximizes the probability of the tree given the data and the model of evolution. You usually get several trees. default starting tree new tree accept a tree with a higher probability 1 generation evaluates probability based on model specified by user evaluates probability based on model specified by user Monte Carlo Markov Chain (MCMC) method -a set of independent searches that occasionally exchange information which allows a search to leap a valley Maximum Likelihood & Bayesian Analysis User postulates a model of evolutionand the program searches for the best tree(s) that are consistent with both the model and with the data (alignment)

  20. Next Week’s Lab Please bring your own laptop!! • Parsimony using a program MESQUITE • Morphology • Build morphological data matrix • Reconstruct a tree via hand • DNA • Align (using Amino Acid as a guide) • Bayesian using a program BEAUTI and BEAST

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